Four base recognition by triplex-forming oligonucleotides at physiological pH

Four base recognition by triplex-forming oligonucleotides at physiological pH

Four base recognition by triplex-forming oligonucleotides at physiological pH

We have achieved recognition of all 4 bp by triple helixformation at physiological pH, using triplex-formingoligonucleotides that contain four different syntheticnucleotides. BAU [20-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizesATbase pairs with high affinity,MeP (3-methyl-2 aminopyridine) binds to GC athigher pHs than cytosine, while APP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one)and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)]bind to CG and TA base pairs, respectively.Fluorescence melting and DNase I footprinting demonstratesuccessful triplex formation at a 19mer oligopurinesequence that contains two CG and two TAinterruptions. The complexes are pH dependent, butare still stable at pH 7.0. BAU, MeP and APP retain considerableselectivity, and single base pair changesopposite these residues cause a large reduction inaffinity. In contrast, S is less selective and toleratesCG pairs as well as TA.

Abstract

We have achieved recognition of all 4 bp by triple helixformation at physiological pH, using triplex-formingoligonucleotides that contain four different syntheticnucleotides. BAU [20-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizesATbase pairs with high affinity,MeP (3-methyl-2 aminopyridine) binds to GC athigher pHs than cytosine, while APP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one)and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)]bind to CG and TA base pairs, respectively.Fluorescence melting and DNase I footprinting demonstratesuccessful triplex formation at a 19mer oligopurinesequence that contains two CG and two TAinterruptions. The complexes are pH dependent, butare still stable at pH 7.0. BAU, MeP and APP retain considerableselectivity, and single base pair changesopposite these residues cause a large reduction inaffinity. In contrast, S is less selective and toleratesCG pairs as well as TA.